Intermittent drying is an influential feature of many arid and temperate rivers and creeks in Australia. While persistent pools represent stable patches recognised to maintain sources of invertebrates in drying creeks, alternative refugia might also be important. The significance of refugia such as in-sediment dormancy that allow invertebrates to maintain viability during dry times have seldom been explored. We tested the importance of in-sediment dormancy and aerial dispersal as alternative refugial mechanisms in both semi-arid and temperate creeks. We predicted distinct invertebrate assemblages between creek types, with colonisation patterns that reflected susceptibility to drying. Both dry sediment and aerial recolonisation were found to be important mechanisms for maintaining diversity, with in-sediment dormancy particularly important in semi-arid creeks. Aerial colonisation was used by a distinct and complimentary set of taxa to those utilising dry sediment. Dry creek beds represented significant short-term refugia for many taxa, with semi-arid creeks showing greater resilience to extended drying. Under climate change available aquatic habitat is expected to decrease, with extended dry periods making alternative refugial mechanisms increasingly important.